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Open data
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Basic information
Entry | Database: PDB / ID: 5xmf | ||||||||||||
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Title | Crystal structure of feline MHC class I for 2,1 angstrom | ||||||||||||
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![]() | IMMUNE SYSTEM / domestic cats / MHC I / Feline immunodeficiency virus / CTL immunity | ||||||||||||
Function / homology | ![]() antigen processing and presentation of peptide antigen via MHC class I / viral budding via host ESCRT complex / antigen processing and presentation / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response ...antigen processing and presentation of peptide antigen via MHC class I / viral budding via host ESCRT complex / antigen processing and presentation / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / viral nucleocapsid / nucleic acid binding / structural constituent of virion / immune response / lysosomal membrane / zinc ion binding / extracellular region Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Liang, R. / Sun, Y. / Wang, J. / Wu, Y. / Zhang, N. / Xia, C. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Major Histocompatibility Complex Class I (FLA-E*01801) Molecular Structure in Domestic Cats Demonstrates Species-Specific Characteristics in Presenting Viral Antigen Peptides Authors: Liang, R. / Sun, Y. / Liu, Y. / Wang, J. / Wu, Y. / Li, Z. / Ma, L. / Zhang, N. / Zhang, L. / Wei, X. / Qu, Z. / Zhang, N. / Xia, C. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 178 KB | Display | ![]() |
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PDB format | ![]() | 139.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.3 KB | Display | ![]() |
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Full document | ![]() | 433.8 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xmmC ![]() 3pwvS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 31947.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 11618.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 993.143 Da / Num. of mol.: 1 / Fragment: UNP residues 40-48 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.42 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: PEG/Ion solution No. 23 (0.2M ammonium formate and 20%(w/v) polyethylene glycol 3,350) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 27016 / % possible obs: 99.55 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.542 / Rsym value: 0.063 / Net I/σ(I): 7.31 |
Reflection shell | Resolution: 2.103→2.157 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 30.971 / Rsym value: 0.063 / % possible all: 99.55 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3PWV Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / SU B: 12.797 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.479 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→50 Å
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Refine LS restraints |
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